From: Ming (ebullience_at_emails.bjut.edu.cn)
Date: Thu Oct 30 2008 - 01:51:16 CDT
Thank you for this discussion! I've understood this point!
>From: "Neelanjana Sengupta" <senguptan_at_gmail.com>
>To: "Peter Freddolino" <petefred_at_ks.uiuc.edu>
>Subject: Re: namd-l: Why there is a bond between the two Hydrogens of the TIP3P
water in Amber force field?
>Date:Thu, 30 Oct 2008 11:09:47 +0530
>I'd like to add that NAMD2.5 would not say anything about the bond being
>ignored, but NAMD2.6 actually gives out a warning message when the TIP3P
>model is used. The message says something like:
>Warning: Ignored 8776 bonds with zero force constants.
>Warning: Will get H-H distance in rigid H2O from H-O-H angle.
>The system has 8776 water molecules. Please let know if this observation is
>On Wed, Oct 29, 2008 at 9:37 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:
>> Purushottam Dixit wrote:
>>> If you are using SHAKE to maintain rigid water conformations (this would
>>> read as 'rigidbonds water' or 'rigidbonds all'), there's a pseudo bond of
>>> high spring constant between the hydrogens. Other than maintaining the
>>> rigidity it has no function.
>> I'm sorry, but this is slightly incorrect. If the water is kept rigid by
>> rigidbonds (using SETTLE, a special constraint solver for TIP3P water) then
>> the bond distances and H-O-H angle are truly constrained (ie, not allowed to
>> vary at all from their equilibrium positions, and having no associated
>> potential); there is no harmonic term here as a spring constant would
>> indicate. The function of the H-H bond, which shows up in water prepared
>> using charmm or amber, is to allow those programs to obtain proper
>> geometries for the rigid water constraints; namd instead calculates the
>> geometry from the O-H equilibrium bond lengths and H-O-H equilibrium angle.
>> Thus, the bond doesn't generally appear in the topology files we distribute,
>> and will be ignored y namd.
>>> On Wed, Oct 29, 2008 at 11:20 AM, Ming <ebullience_at_emails.bjut.edu.cn<mailto:
>>> ebullience_at_emails.bjut.edu.cn>> wrote:
>>> Dear all,
>>> I am trying to simulate my system using namd with the amber-style
>>> force field.
>>> Everything was fine! However I found there is a bond between the
>>> two Hydrogens of
>>> the TIP3P water in Amber force field. For what reason they put a
>>> bond between the
>>> two Hydrogen? Any comments? Thanks in advance!
>Neelanjana Sengupta, PhD
>Physical and Materials Chemistry Division
>National Chemical Laboratory
>Dr. Homi Bhaba Road
>Pune 411008, India
>Phone: +91-20-2590 2087
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